[BioC] GSEABase on none affy data/mapping problem(?)
Martin Morgan
mtmorgan at fhcrc.org
Mon Jun 22 12:26:58 CEST 2009
Hi Lina --
"Lina Cekaite" <Lina.Cekaite at rr-research.no> writes:
> Hi Martin,
>
> You were right, my ExpressionSet lacked the annotation and when I added
> it, GeneSetCollection() worked. Thanks a lot.
>
> One GSEABase following up question, I would like to have GeneSymbl on
> the heatmaps instead of probeIds, is it possible to change it that using
> KEGG2heatmap()?
It might be easiest for you to write a small function to do this; look
at the output of
showMethods(KEGG2heatmap, includeDef=TRUE)
for some ideas. The mapping between probe and symbol is not 1:1, so
this might introduce problems that you would need to solve. Others on
the list might have better ideas.
Martin
> Lina
>
> -----Original Message-----
> From: Martin Morgan [mailto:mtmorgan at fhcrc.org]
> Sent: Sunday, June 21, 2009 6:12 AM
> To: Lina Cekaite
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] GSEABase on none affy data/mapping problem(?)
>
> Hi Lina --
>
> "Lina Cekaite" <Lina.Cekaite at rr-research.no> writes:
>
>> Dear all,
>>
>> I am having problems to run GSEA on none affy data and wonder if
> someone
>> could help. I made an annotation library mapping EntrezIDs using
>> AnnotationDbi and I am able to run KEGG using the custom annotated
>>
>> package "AB1700sp2.db". But I would like to run trough
>> GeneSetCollections()and there I need to map probe IDs to EntrezIDs and
>> then do GeneSetCollections().I tried both make an annotated gene set
> or
>> by using ExpressionSet, but end up with the same type of error.
>
> It sounds like you have made a package AB1700sp2.db that successfuly
> maps from your probeset identifiers to Entrez identifiers. If so, then
>
> GeneSetCollection(CRCsubset_map_Q_unique, setType=KEGGCollection())
>
> should work. This requires that annotation(CRCsubset_map_Q_unique)
> returns the name of your custom annotation package, i.e.,
> "AB1700sp2.db".
>
> Martin
>
>>
>>
>> Any ideas what is wrong?
>>
>>
>>
>> Best, Lina
>>
>>
>>
>> ExpressionSet
>>
>>> CRCsubset_map_Q_unique
>>
>> ExpressionSet (storageMode: lockedEnvironment)
>>
>> assayData: 19755 features, 50 samples
>>
>> element names: exprs, se.exprs
>>
>> phenoData
>>
>> sampleNames: A1_PT, A17_PT, ..., A54_NT (50 total)
>>
>> varLabels and varMetadata description:
>>
>> samplename: read from file
>>
>> assayname: read from file
>>
>> group: read from file
>>
>> featureData
>>
>> featureNames: 160832, 105812, ..., 221132 (19755 total)
>>
>> fvarLabels and fvarMetadata description: none
>>
>> experimentData: use 'experimentData(object)'
>>
>> Annotation:
>>
>>
>>
>>> ## Probe annotation to Entrez ids
>>
>>> probeIds <- featureNames(CRCsubset_map_Q_unique)
>>
>>> geneIds <- getEG(probeIds, "AB1700sp2")
>>
>>> gs1<-GeneSet(EntrezIdentifier(), setName="sample.GeneSet2",
>> setIdentifier="101",
>>
>> + geneIds=geneIds)
>>
>>> ## End(Not run)
>>
>>> ## Create a new identifier
>>
>>> setClass("FooIdentifier",
>>
>> + contains="GeneIdentifierType",
>>
>> + prototype=prototype(
>>
>> + type=new("ScalarCharacter", "Foo")))
>>
>> [1] "FooIdentifier"
>>
>>> ## Create a constructor (optional)
>>
>>> FooIdentifier <- function() new("FooIdentifier")
>>
>>> geneIdType(FooIdentifier())
>>
>> "Foo"
>>
>>> ## tidy up
>>
>>> removeClass("FooIdentifier")
>>
>> [1] TRUE
>>
>>>
>>
>>> gs1
>>
>> setName: sample.GeneSet2
>>
>> geneIds: 1, 10, ..., 9997 (total: 19755)
>>
>> geneIdType: EntrezId
>>
>> collectionType: Null
>>
>> details: use 'details(object)'
>>
>>>
>>
>>>
>>
>>> gsc<-GeneSetCollection(gs1, idType=EntrezIdentifier(),
>> setType=KEGGCollection())
>>
>> Error in function (classes, fdef, mtable) :
>>
>> unable to find an inherited method for function "GeneSetCollection",
>> for signature "GeneSet", "EntrezIdentifier", "KEGGCollection"
>>
>>>
>>
>>> traceback()
>>
>> 3: stop("unable to find an inherited method for function \"",
>> fdef at generic,
>>
>> "\", for signature ", cnames)
>>
>> 2: function (classes, fdef, mtable)
>>
>> {
>>
>> methods <- .findInheritedMethods(classes, fdef, mtable)
>>
>> if (length(methods) == 1L)
>>
>> return(methods[[1L]])
>>
>> else if (length(methods) == 0L) {
>>
>> cnames <- paste("\"", sapply(classes, as.character),
>>
>> "\"", sep = "", collapse = ", ")
>>
>> stop("unable to find an inherited method for function \"",
>>
>> fdef at generic, "\", for signature ", cnames)
>>
>> }
>>
>> else stop("Internal error in finding inherited methods; didn't
>> return a unique method")
>>
>> }(list("GeneSet", "EntrezIdentifier", "KEGGCollection"), function
>> (object,
>>
>> ..., idType, setType)
>>
>> standardGeneric("GeneSetCollection"), <environment>)
>>
>> 1: GeneSetCollection(gs1, idType = EntrezIdentifier(), setType =
>> KEGGCollection())
>>
>>
>>
>>>
>>
>>> map <- getAnnMap("ENTREZID", "AB1700sp2.db", load=TRUE, type=c("db"))
>>
>>> gsc<-GeneSetCollection(CRCsubset_map_Q_unique,
>> idType=map,setType=KEGGCollection())
>>
>> Error in function (classes, fdef, mtable) :
>>
>> unable to find an inherited method for function "GeneSetCollection",
>> for signature "ExpressionSet", "AnnDbBimap", "KEGGCollection"
>>
>>>
>>
>>> traceback()
>>
>> 3: stop("unable to find an inherited method for function \"",
>> fdef at generic,
>>
>> "\", for signature ", cnames)
>>
>> 2: function (classes, fdef, mtable)
>>
>> {
>>
>> methods <- .findInheritedMethods(classes, fdef, mtable)
>>
>> if (length(methods) == 1L)
>>
>> return(methods[[1L]])
>>
>> else if (length(methods) == 0L) {
>>
>> cnames <- paste("\"", sapply(classes, as.character),
>>
>> "\"", sep = "", collapse = ", ")
>>
>> stop("unable to find an inherited method for function \"",
>>
>> fdef at generic, "\", for signature ", cnames)
>>
>> }
>>
>> else stop("Internal error in finding inherited methods; didn't
>> return a unique method")
>>
>> }(list("ExpressionSet", "AnnDbBimap", "KEGGCollection"), function
>> (object,
>>
>> ..., idType, setType)
>>
>> standardGeneric("GeneSetCollection"), <environment>)
>>
>> 1: GeneSetCollection(CRCsubset_map_Q_unique, idType = map, setType =
>> KEGGCollection())
>>
>>>
>>
>>> sessionInfo()
>>
>> R version 2.9.0 (2009-04-17)
>>
>> i386-pc-mingw32
>>
>>
>>
>> locale:
>>
>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>> States.1252;LC_MONETARY=English_United
>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>
>>
>>
>> attached base packages:
>>
>> [1] tools stats graphics grDevices utils datasets
> methods
>> base
>>
>>
>>
>> other attached packages:
>>
>> [1] GO.db_2.2.11 KEGG.db_2.2.11 Ruuid_1.22.0
>> GSEABase_1.6.0 RBGL_1.20.0
>>
>> [6] graph_1.22.2 genefilter_1.24.0 Category_2.10.0
>> annotate_1.22.0 RColorBrewer_1.0-2
>>
>> [11] AB1700sp2.db_1.0.0 RSQLite_0.7-1 DBI_0.2-4
>> AnnotationDbi_1.6.0 Biobase_2.4.1
>>
>>
>>
>> loaded via a namespace (and not attached):
>>
>> [1] splines_2.9.0 survival_2.35-4 XML_2.5-1 xtable_1.5-5
>>
>>
>>
>> Lina Cekaite, PhD
>>
>> Department of Cancer Prevention
>>
>> Rikshospitalet University Hospital
>>
>> Faculty Division, The Norwegian Radium Hospital,
>>
>> University of Oslo, 0316 Oslo
>>
>> NORWAY
>>
>>
>>
>> Email: linac at rr-research.no
>>
>>
>>
>>
>> [[alternative HTML version deleted]]
>>
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--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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